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Questions tagged [phylogenetics]

A sub-discipline of evolutionary biology which involves the study of evolutionary relatedness between different organisms based on their molecular and morphological features.

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How to determine the number of parameters in a phylogenetic model?

I want to calculate the AIC for a phylogeny that I inferred via maximum likelihood. To calculate the AIC I need to know the number of parameters in the model. But how do I determine this?
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30 views

Have traditional categories such as phylum, class, genus, been dispensed with in modern taxonomy?

Looking through the one zoom and EOL projects I see no reference to such categories.
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22 views

Where can I find datasets containing large phylogenetic networks?

There are many datasets out there for phylogenetic trees, one can example can be found here. However, I couldn't find something for phylogenetic networks. According to Wikipedia: A phylogenetic ...
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83 views

The protostome/deuterostome distinction and why it is important

As I unerstand it, at some point an embryo develops a hole; this hole continues to punch through, and eventually makes an opening at the other side of the embryo. If the original hole becomes the ...
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36 views

Basic question about phylogenetic trees

The following is an illustration rom my book of the phylogenetic tree of 6 animal phyla (the red stuff is mine): I think what's causing some confusion is that there are no names/years at the circled ...
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What is the closest relative to odd-toed ungulate?

I have seen about 3 variation of phylogenetic tree about odd-toed ungulate and I don't know which one is really updated or outdated or which one have more backed up theory First is odd-toed ungulate ...
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2answers
25 views

The parts of the phylogenetic nomenclature that need to be “unique”

I am not quite sure I have sorted through the diversity of approaches to nomenclature, but I had a specific question to help clarify what is going on. Basically I am just wondering what needs to be ...
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28 views

Example Clade Names in PhyloCode

After looking through the PhyloCode, the only thing I found that looked like an example was in Article 9, Chapter 4: A node-based definition may be abbreviated "<A&B" or "<A&B&C&...
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54 views

What could explain discrepancies between dates provided by the fossil record vs. the molecular clock?

I am studying a mud snail genus called Ecrobia. For the Caspian species (Ecrobia grimmi), there is a discrepancy between dates provided by the fossil record and the molecular clock: First appearance ...
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Why the SNPs from the earliest human haplogroups are missing in people outside of Africa if they are infact the descendants of it?

The SNPs M91, P97, M31, P82, M23, M114, P262, M32, M59, P289, P291, P102, M13, M171, M118 from haplogroup A and SNPs M60, M181, P90 from haplogroup B are missing in people without recent African ...
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Estimating population divergence time with a single mitochondrial marker

Is it possible to estimate population divergence time with a single mitochondrial marker? Here is additional information for my specific case: Mitochondrial marker: Cytochrome Oxidase Subunit 1 (...
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45 views

How would I represent this on a cladogram?

So, right now I am making a cladogram (More of a dendrogram) for a kingdom of fictional species, and I'm not exactly sure how to represent a certain relationship. Let's say that the oldest class in ...
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Are there any open phylogenetic projects that don't require coding to make a contribution

I am stay at home learner, not pursuing education formal education and currently doing a part time job. I've however completed masters in biotechnology and I'm studying to pursue PhD in molecular ...
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49 views

MLE estimation with Mk model in ape or phangorn?

When doing MLE with the R package ape or phangorn, is it possible to set the substitution model to Mk? If so, how does one do this?
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45 views

Minimum number of clades needed to partition Vertebrates while maintaining Birds, Mammals, and Amphibians as distinct clades?

At school I was taught the Linnaean view of vertebrate life - that vertebrate animals consisted of 5 distinct groups: mammals, birds, reptiles, amphibians, fish. I learned later however that this was ...
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How does one go from a couple of DNA sequences to a distance-matrix?

For a project we need to explain the subject of UPGMA. We think we understand thee method itself but I fail to see how you go from a number of DNA-sequences to the distance matrix. I understand ...
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45 views

Finding different Proteins with same function [closed]

Could you help me about finding two different proteins that coming from different ancestors, perform same function? Thank you
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17 views

Is there a distinction between linkage phase and haplotype?

Linkage phase- combination of alleles that are coinherited Haplotype- combination of alleles an organism has at different loci. So could an informative meiosis be defined as a meiosis in which a ...
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If we sequenced the genome of every species, would all phylogenies agree?

The Tree of Life is still up for debate. Most of this debate seems to be due to a lack of genomic information, but that deficiency is decreasing rapidly with advances in technology and sequencing ...
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1answer
196 views

Forming a cladogram from a table of information

Can someone please give me some tips or help me build a cladogram from the following table of information? The outgroup is Lancelets and the first derived character is vertebrae, followed by Lampreys ...
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2answers
27 views

Is “Monophyly” context dependent?

I am thinking about this thought experiment: Suppose we have three taxa which are grouped into the following tree: {{A,B},C}, clearly {B,C} is a paraphyletic group. But if A go extinct in the near ...
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53 views

In what does Genetic clustering and Cline sharpness differ?

They are both ways to measure divergence in species but I'm not understanding in what exactly the differ if both use hybrid zones and gene frequencies in the study.
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34 views

how origin of koi carp is different from goldfish

where did koi-carp originate? how are they different from goldfish? Wikipedia say that goldfish originated by genetic mutation but what about koi-carps?
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Did unikonts come from bikonts, are we sure, and how did we lose a “kont”?

Layperson's question here. It seems from what I read that it's pretty agreed-upon that bikonts preceeded unikonts, that unikonts descended from bikonts, and that both have mitochondria or potentially-...
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Why outgroups are supposed to be ancestral?

I was reading about phylogenies and found many literatures said that outgroups contain the ancestrial trait, but why is that? Aren't they also experiencing the same amount of evolutionary time and (...
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2answers
389 views

When did birds and mammals diverge?

Which was the most recent common ancestor between mammals and birds? Form a rapid google research I could not find good answers. This site seems to imply it was at least 250 milions of years ago. ...
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Did insects and arachnids diverge before or after moving to land?

Question: Are arachnids and insects so distantly related that they were already diverging before their (independent) emergence(s) on land? I am curious to know what the fossil record and molecular ...
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1answer
85 views

How would homologous recombination and mutations affect speciation?

I'm wondering how homologous recombination and mutations can affect how speciation can occur from one species (so that 2 will be created). I'm doing research and I found that different mutations and ...
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37 views

Question about phylogenies and DNA sequencing

I'm reading this web page which talks about phylogenies and DNA sequencing: https://bioinf.comav.upv.es/courses/biotech3/theory/phylogeny.html A certain sentence says, "If we consider dolphins and ...
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1answer
24 views

Is it possible for parsimony to estimate more state changes than stochastic character mapping

I'm mapping states (geographic regions) onto a phylogeny to estimate the number of transmissions between countries. I'm using two methods, stochastic character mapping implemented in Phytools and ...
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1answer
99 views

Finding phylogenetic distance between sequences?

I'm working on a piece of software that does comparative genomic analysis; and I found out in homology methods for functional annotation, it's preferable to pick the high scoring homolog from a ...
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1answer
22 views

computing relative synonymous codon usage from a coding sequence alignment while accounting for phylogenetic inertia?

I would like to compute the relative synonymous codon usage (RSCU) from coding sequence alignments. But since the coding sequences from an alignment are not independent realization, the statistics (...
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1answer
99 views

More informative phylogenetic trees

In the presentation of phylogenetic trees, the geometric shape of the trees often seems somehow arbitrary and is more driven by aesthetics than by informative reasons. But wouldn't it make sense to ...
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1answer
104 views

Has the most recent common ancestor of all living birds lived after dinosaur mass extinction?

I wonder if one or more phylogenetic threads of dinosaurs survived the mass extinction. In other words, are all living birds equally related to any given ancient dinosaur, or do some birds relate ...
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“50% of the variance in antisocial phenotypes is the result of genetic factors” means what?

How can i understand the following sentence: Overall, the conclusions reached by these studies have been highly consistent in showing that approximately 50% of the variance in antisocial phenotypes ...
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2answers
160 views

Did Carl Linnaeus ever name a species he never saw?

According to this post Carl Linnaeus named more than 13,000 species which is definitely quite impressive. If we consider a 50 years career it makes about 5 species per week! It would feel impressive ...
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423 views

How to interpret weighted Robinson-Foulds distance between phylogenies?

The Robinson-Foulds (RF) metric provides symmetric distance between two phylogenies as a sum of monophyletic groups present in one tree but not in the other. The normalised RF distance is given as $\...
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83 views

Manipulating phylogenetic trees

I am looking to manipulate manually constructed phylogenetic trees (adding bootstrap values, markers to indicate trate loss/gain etc.) I came across a paper that used Macclade, however, this no longer ...
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Classification and differences between homologous, homoplastic, analogous, derived and ancestral traits?

My question is contextualised for basic phylogeny knowledge. Here is my understanding: similar or identical traits between any two species, at the basic level, can be either homologous, meaning the ...
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What is the difference between phylogroup and subclade? [closed]

Looking for clarification in terminology, examples would be greatly appreciated! Not sure how this is off-topic. It is a general question about the difference between biological concepts defined in ...
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2answers
90 views

Could homoplasy occur within a clade?

Consider the below phylogeny. taxon1 and 2 are sister taxa but: - share a brown color coat - differ from their closest common ancestor (light color coat) Is this a case of homoplasy (Analogous trait)?...
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How to choose the most appropriate measure of genetic distance

I am conducting a phylogeography study of a fish species and am trying to construct a phylogenetic tree to describe population structure and ancestry. I have constructed trees using various measures ...
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1answer
864 views

Bootstrap values

What do the bootstrap values indicate about the relationship between the species? I'm working on Mega program but I don;t understand what bootstrap value means in simple terms and also what does it ...
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2answers
218 views

What is the function of multiple nuclei in syncytial cells?

What is the function of multiple nuclei in syncytial cells specially in protists with cilia? Is multiple nuclei a special characteristics of only ciliated cells?
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124 views

Phylogenetic Independent Contrasts with discrete traits

I understand that PICs are normally only used for continuous traits. However, on this how-to site (https://www.r-phylo.org/wiki/HowTo/Phylogenetic_Independent_Contrasts) there is mention of "Discrete ...
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3answers
10k views

Branch length in phylogenetic trees

I know this is a very basic question, but it is not too clear to me what is the unit of measure of branch length in phylogenetic trees. I have come to understand that it is usually expressed in number ...
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1answer
82 views

What is the difference between phylogenetic tree “construction” and “reconstruction”?

When I look through papers, there are two terms Phylogenetic tree construction Phylogenetic tree "Re"construction What is the difference between phylogenetic tree "construction" and "reconstruction" ...
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1answer
85 views

How to use a published phylogenetic tree?

I would like to know how should I use a phylogenetic tree from an already published article, to put it on my own article so I can analyze the evolution of a trait. Is there any software I can use, or ...
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1answer
356 views

Which nucleotide as start point for maximum parsimony?

Background Maximum parsimony is used to build an evolutionary tree by choosing the "simplest" one. I see a lot of examples about how this should be done. For example: Question However it's not clear ...
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Infer distance since duplication from tree?

Question I have a really simple question, but I'm not able to figure it out. I made a tree (using BLOSUM62). Here is a part of the tree: How can I calculate the distance till the duplication ...